DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations

Autores
Cuzzolin, Alberto; Sturlese, Mattia; Malvacio, Ivana; Ciancetta, Antonella; Moro, Stefano
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Virtual screening (VS) is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS) exploits knowledge about the three-dimensional (3D) structure of protein targets and uses the docking methodology as search engine for novel hits. The success of a SBVS campaign strongly depends upon the accuracy of the docking protocol used to select the candidates from large chemical libraries. The identification of suitable protocols is therefore a crucial step in the setup of SBVS experiments. Carrying out extensive benchmark studies, however, is usually a tangled task that requires users' proficiency in handling different file formats and philosophies at the basis of the plethora of existing software packages. We present here DockBench 1.0, a platform available free of charge that eases the pipeline by automating the entire procedure, from docking benchmark to VS setups. In its current implementation, DockBench 1.0 handles seven docking software packages and offers the possibility to test up to seventeen different protocols. The main features of our platform are presented here and the results of the benchmark study of human Checkpoint kinase 1 (hChk1) are discussed as validation test.
Fil: Cuzzolin, Alberto. Università di Padova; Italia
Fil: Sturlese, Mattia. Università di Padova; Italia
Fil: Malvacio, Ivana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Ciancetta, Antonella. Università di Padova; Italia
Fil: Moro, Stefano. Università di Padova; Italia
Materia
DOCKING BENCHMARK
MOLECULAR DOCKING
STRUCTURE-BASED DRUG DESIGN
VIRTUAL SCREENING
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/52602
Acceder
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spelling DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulationsCuzzolin, AlbertoSturlese, MattiaMalvacio, IvanaCiancetta, AntonellaMoro, StefanoDOCKING BENCHMARKMOLECULAR DOCKINGSTRUCTURE-BASED DRUG DESIGNVIRTUAL SCREENINGhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1Virtual screening (VS) is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS) exploits knowledge about the three-dimensional (3D) structure of protein targets and uses the docking methodology as search engine for novel hits. The success of a SBVS campaign strongly depends upon the accuracy of the docking protocol used to select the candidates from large chemical libraries. The identification of suitable protocols is therefore a crucial step in the setup of SBVS experiments. Carrying out extensive benchmark studies, however, is usually a tangled task that requires users' proficiency in handling different file formats and philosophies at the basis of the plethora of existing software packages. We present here DockBench 1.0, a platform available free of charge that eases the pipeline by automating the entire procedure, from docking benchmark to VS setups. In its current implementation, DockBench 1.0 handles seven docking software packages and offers the possibility to test up to seventeen different protocols. The main features of our platform are presented here and the results of the benchmark study of human Checkpoint kinase 1 (hChk1) are discussed as validation test.Fil: Cuzzolin, Alberto. Università di Padova; ItaliaFil: Sturlese, Mattia. Università di Padova; ItaliaFil: Malvacio, Ivana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Ciancetta, Antonella. Università di Padova; ItaliaFil: Moro, Stefano. Università di Padova; ItaliaMolecular Diversity Preservation International2015-06-29info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/52602Cuzzolin, Alberto; Sturlese, Mattia; Malvacio, Ivana; Ciancetta, Antonella; Moro, Stefano; DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations; Molecular Diversity Preservation International; Molecules; 20; 6; 29-6-2015; 9977-99931420-30491420-3049CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.mdpi.com/1420-3049/20/6/9977info:eu-repo/semantics/altIdentifier/doi/10.3390/molecules20069977info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:26:58Zoai:ri.conicet.gov.ar:11336/52602instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 14:26:58.579CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations
title DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations
spellingShingle DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations
Cuzzolin, Alberto
DOCKING BENCHMARK
MOLECULAR DOCKING
STRUCTURE-BASED DRUG DESIGN
VIRTUAL SCREENING
title_short DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations
title_full DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations
title_fullStr DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations
title_full_unstemmed DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations
title_sort DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations
dc.creator.none.fl_str_mv Cuzzolin, Alberto
Sturlese, Mattia
Malvacio, Ivana
Ciancetta, Antonella
Moro, Stefano
author Cuzzolin, Alberto
author_facet Cuzzolin, Alberto
Sturlese, Mattia
Malvacio, Ivana
Ciancetta, Antonella
Moro, Stefano
author_role author
author2 Sturlese, Mattia
Malvacio, Ivana
Ciancetta, Antonella
Moro, Stefano
author2_role author
author
author
author
dc.subject.none.fl_str_mv DOCKING BENCHMARK
MOLECULAR DOCKING
STRUCTURE-BASED DRUG DESIGN
VIRTUAL SCREENING
topic DOCKING BENCHMARK
MOLECULAR DOCKING
STRUCTURE-BASED DRUG DESIGN
VIRTUAL SCREENING
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Virtual screening (VS) is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS) exploits knowledge about the three-dimensional (3D) structure of protein targets and uses the docking methodology as search engine for novel hits. The success of a SBVS campaign strongly depends upon the accuracy of the docking protocol used to select the candidates from large chemical libraries. The identification of suitable protocols is therefore a crucial step in the setup of SBVS experiments. Carrying out extensive benchmark studies, however, is usually a tangled task that requires users' proficiency in handling different file formats and philosophies at the basis of the plethora of existing software packages. We present here DockBench 1.0, a platform available free of charge that eases the pipeline by automating the entire procedure, from docking benchmark to VS setups. In its current implementation, DockBench 1.0 handles seven docking software packages and offers the possibility to test up to seventeen different protocols. The main features of our platform are presented here and the results of the benchmark study of human Checkpoint kinase 1 (hChk1) are discussed as validation test.
Fil: Cuzzolin, Alberto. Università di Padova; Italia
Fil: Sturlese, Mattia. Università di Padova; Italia
Fil: Malvacio, Ivana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Ciancetta, Antonella. Università di Padova; Italia
Fil: Moro, Stefano. Università di Padova; Italia
description Virtual screening (VS) is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS) exploits knowledge about the three-dimensional (3D) structure of protein targets and uses the docking methodology as search engine for novel hits. The success of a SBVS campaign strongly depends upon the accuracy of the docking protocol used to select the candidates from large chemical libraries. The identification of suitable protocols is therefore a crucial step in the setup of SBVS experiments. Carrying out extensive benchmark studies, however, is usually a tangled task that requires users' proficiency in handling different file formats and philosophies at the basis of the plethora of existing software packages. We present here DockBench 1.0, a platform available free of charge that eases the pipeline by automating the entire procedure, from docking benchmark to VS setups. In its current implementation, DockBench 1.0 handles seven docking software packages and offers the possibility to test up to seventeen different protocols. The main features of our platform are presented here and the results of the benchmark study of human Checkpoint kinase 1 (hChk1) are discussed as validation test.
publishDate 2015
dc.date.none.fl_str_mv 2015-06-29
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/52602
Cuzzolin, Alberto; Sturlese, Mattia; Malvacio, Ivana; Ciancetta, Antonella; Moro, Stefano; DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations; Molecular Diversity Preservation International; Molecules; 20; 6; 29-6-2015; 9977-9993
1420-3049
1420-3049
CONICET Digital
CONICET
url http://hdl.handle.net/11336/52602
identifier_str_mv Cuzzolin, Alberto; Sturlese, Mattia; Malvacio, Ivana; Ciancetta, Antonella; Moro, Stefano; DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations; Molecular Diversity Preservation International; Molecules; 20; 6; 29-6-2015; 9977-9993
1420-3049
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.mdpi.com/1420-3049/20/6/9977
info:eu-repo/semantics/altIdentifier/doi/10.3390/molecules20069977
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Molecular Diversity Preservation International
publisher.none.fl_str_mv Molecular Diversity Preservation International
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.22299

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